Chymeric Tutorials

Do awesome stuff - awesomely.

How-To: NeuroGentoo

| Comments | Edit

Gentoo

Gentoo linux is a modern, extremely flexible, and very transparent linux distribution. Among many other things it provides:

  • Rolling releases (continuous versioning, in brief: no tedious “OS version updates” for you - ever)
  • Building from source (custom geared for every machine - from ancient laptop to data-analysis power-box)
  • Seamless support for live source packages (get that very latest version with that one new function that solves all your problems - directly from the source code upstream wrote 5 minutes ago!)

Cutting the Gentoo publicity short, and getting to the point: Gentoo is awesome for science.

Neuro

Already In!

Sadly, until July 2013 Gentoo provided almost no neuroscience software. In response, we started writing up some ebuilds for popular neuroscience (mainly neuropsychology, to be precise) software packages. With the help of a handful of enthusiastic Gentoo-Science overlay maintainers we have managed to help Portage bring you up-to-date and development versions of the following software packages (in order of ebuild pull):

  • sci-biology/psychopy
  • sci-biology/pybrain
  • sci-libs/nipy
  • sci-libs/nipype
  • sci-libs/nibabel
  • sci-libs/pydicom
  • sci-biology/mne-python
  • sci-biology/pysurfer

Which you can conveniently access over the popular and stable gentoo-science overlay. To enable the overlay we suggest you follow the “Manually setting overlay locations” instructions from the Gentoo overlay guide. In short, the procedure is:

  1. Add PORTDIR_OVERLAY="/usr/local/portage/sci" (or whatever directory you prefer) to your /etc/portage/make.conf file.
  2. Run git clone https://github.com/gentoo-science/sci.git /usr/local/portage/sci (or whatever other directory you previously chose).

There - wasn’t that easy?

Work In Progress:

But all is not always fun and games in the world of NeuroGentoo. Arguably the most important software packages for neuropsychology and brain imaging - AFNI, FSL, and SPM - got stuck in the pull phase. Apparently the packages do not really meet Gentoo security, build, and file management exigences and need to be patched - quite a bit. The Project is community-lead, and help would be much appreciated!

But the good news is: The packages kind of work! Not yet well enough for the gentoo-science overlay, but perhaps well enough for you and me. So, these are the packages we are still working on (and which you can already use):

While officially unsupported, these packages are just as easy to get as the supported ones. You can simply merge the NeuroGentoo branch from our gentoo-science fork into your local gentoo-science repository. After following the gentoo-science overlay instructions from the previous section, run:

1
2
3

cd /usr/local/portage/sci
git remote add chymera https://github.com/TheChymera/sci.git
git pull chymera neurogentoo

NeuroGentoo!

Now that you have read, understood, and followed the instructions above - How-To: NeuroGentoo boils down to the following:

Emerge!

The stable versions are at your fingertips - and if you want the cutting-edge development versions you can just tell Portage.

1

# emerge psychopy

Contribute!

Yes, NeuroGentoo is supported by Gentoo users and neuroscientists (if you are here you might well be at least one of those) - we do not have paid employees nor do we make a direct profit from this. We contribute because neuroscience is important and Gentoo is awesome!

Please submit patches and contribute to the pull requests for AFNI, FSL, and SPM!

Additional packages are welcome, and we would recommend you submit pull requests directly to gentoo-science. We will however gladly include any working ebuilds in our overlay - if they take too long to get into gentoo-science.

Credits

The Neurogentoo initiative is coordinated by Horea Christian, and contributors include François Bissey and Martin Luessi.

Comments